Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.

Macina, Roberto A.; Morii, Ken; Hu, Xue-Lan; Negorev, Dmitri; Spais, Chrysanthe; Ruthig, Lisa A.; Riethman, Harold

doi:10.1101/gr.5.3.225

Cited by 25 publications

(24 citation statements)

References 40 publications

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“…Data on polymorphic telomeres are from Riethman, unpubl. results;Wilke et al (1991); Ijdo et al (1992); Cook et al (1994); Macina et al (1994Macina et al ( , 1995; Martin-Gallardo et al (1995); Reston et al (1995); Monfouilloux et al (1998);Trask et al (1998);van Overveld et al (2000). sequences were not already identified by the BLAST analysis described above; for the most part, the regions identified by WSSD were consistent with our analyses, although each method missed a small percentage of the duplications.…”

Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 80%

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Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

117

119

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Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within ∼10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions

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Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 80%

“…Large variant alleles of many human subtelomeric regions exist, and are believed to consist entirely of subtelomeric repeats (Wilkie et al 1991;Macina et al 1994Macina et al , 1995Trask et al 1998;Mefford and Trask 2002). For example, Wilkie et al (1991) found that three alleles varying in length up to 260 kb exist at the 16p telomere.…”

mentioning

confidence: 99%

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

117

119

View full text Add to dashboard Cite

show abstract

“…Because the presence/absence of fluorescent signals indicates the gain/loss of segments that are several tens of kilobases long, this variability is most probably related to size polymorphisms known to affect some chromosome ends (Brown et al 1990). For instance, the relatively rare 6qter-DNF92 variant P observed here may correspond to, and perhaps completely explain, the long 6qter allele described by Macina et al (1995). Similarly, the four 16pter variants distinguished here by FISH techniques may be related to the length polymorphism found for this chromosome end (Wilkie et al 1991).…”

Section: Discussionmentioning

confidence: 92%

Segmental Polymorphisms in the Proterminal Regions of a Subset of Human Chromosomes

Der-Sarkissian¹,

Vergnaud²,

Borde³

et al. 2002

Genome Res.

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The subtelomeric domains of chromosomes are probably the most rapidly evolving structures of the human genome. The highly variable distribution of large duplicated subtelomeric segments has indicated that frequent exchanges between nonhomologous chromosomes may have been taking place during recent genome evolution. We have studied the extent and variability of such duplications using in situ hybridization techniques and a set of well-defined subtelomeric cosmid probes that identify discrete regions within the subtelomeric domain. In addition to reciprocal translocation and illegitimate recombination events that could explain the observed mosaic pattern of subtelomeric regions, it is likely that homology-based recombination mechanisms have also contributed to the spread of distal subtelomeric sequences among particular groups of nonhomologous chromosome arms. The frequency and distribution of large-scale subtelomeric polymorphisms may have direct implications for the design of chromosome-specific probes that are aimed at the identification of cryptic subtelomeric deletions. Furthermore, our results indicate that the relevance of some of the telomere closures proposed within the present Human Genome Sequence draft are restricted to specific allelic variants of unknown frequencies

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“…The commercial 2ptel probe (Vysis) is obtained by Alu-PCR from the 340 kb half-YAC clone yRM2052, presumably containing the terminal 320 kb of chromosome 2p, as one of its ends (U32389) maps at chr2:322536 -322595. 12 As telomeric FISH markers can be located even at 300 -400 kb proximal to the telomeric end, we postulated that the preservation of tel2p probe signals could represent either a single-copy region between the duplicated portion and a more distal deleted region or the start point of the duplicated region. Further experiments demonstrated that the second alternative was correct: the probe overlaps both the deleted segment and a portion of the duplicated sequence.…”

Section: Discussionmentioning

confidence: 99%

A familial inverted duplication/deletion of 2p25.1–25.3 provides new clues on the genesis of inverted duplications

et al. 2008

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We studied a family in which the same 10 Mb inverted duplication of 2p25.3 -p25.1 segregates in two children and their father, all showing a trisomy phenotype. As FISH analysis demonstrated that the duplication was inverted, we suspected that a contiguous terminal deletion was also present, according to the classical inv dup del type of rearrangements. Although FISH with 2p and 2q subtelomeric probes gave normal results, 100 kb resolution array-C\GH (aCGH) showed that, beside the duplication, a 273 kb deletion was also present. The presence of a single-copy region between the deleted and duplicated regions was further suspected through high-resolution aCGH analysis (B20 kb), although only one informative spot having a normal log ratio was detected. The precise structure of the rearrangement was re-defined by real-time PCR and breakpoint cloning, demonstrating the presence of a 2680 bp single-copy sequence between deleted and duplicated regions and the involvement of a simple repeat with the potential for forming a non-B DNA structure. The rearrangement was not mediated by segmental duplications or short inverted repeats, and the double-strand break might have been repaired by nonhomologous end joining or microhomology-mediated intrastrand repair. These data highlight the fact that concomitant deletions associated with inverted duplications are very likely to be more frequent than classical cytogenetic methods alone have been able to demonstrate. The phenotypic effects of the trisomy and of the terminal 2p deletion are discussed.

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Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.

Cited by 25 publications

References 40 publications

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Segmental Polymorphisms in the Proterminal Regions of a Subset of Human Chromosomes

A familial inverted duplication/deletion of 2p25.1–25.3 provides new clues on the genesis of inverted duplications

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